GSR: Simulator - invertFREGENE

Basic Package Attributes
AttributeValue
Title invertFREGENE
Short Description InvertFREGENE is a forward-in-time simulator of inversions in population genetic data
Long Description invertFREGENE is the forward-in-time simulator of inversions in population genetic data, while SAMPLE samples genotype and haplotype data from the output of invertFREGENE simulations based on specified individual and marker ascertainment criteria, including a continuous and case-control disease model. invertFREGENE has been developed from a beta version of the population genetic simulator FREGENE, and as a result there are a small number of features not included in invertFREGENE (eg. it does not model natural selection), therefore we provide self-contained documentation for invertFREGENE. O'Reilly PF, Coin LJ, Hoggart CJ. invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics. 2010 Mar 15;26(6):838-40.
Project Started 2009
Last Release 10 years, 11 months ago
Homepagehttp://www.ebi.ac.uk/projects/BARGEN/
Citations O'Reilly PF, Coin LJ, Hoggart CJ, invertFREGENE: software for simulating inversions in population genetic data., Bioinformatics, 03-15-2010 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
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Last evaluated05-02-2019 (534 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation, Inversion and Rearrangement (Inversion),
Simulation MethodForward-time,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence, Phenotypic Trait (Using sample), Demographic, Diversity Measures,
Sequencing Reads
File FormatProgram Specific,
Sample TypeRandom or Independent, Case-control (Using sample),
Phenotype
Trait TypeQuantitative (Using sample),
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Bottleneck (Using consecutive invertfregene simulations), User Defined (Using consecutive invertfregene simulations),
Gene FlowIsland Models, User-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
DeterminantSingle-locus, Multi-locus,
ModelsMulti-locus models,
RecombinationUniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation ModelsTwo-allele Mutation Model,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsLinux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

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